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Analysis of the loop-helix interaction in bundle motif protein structures
T B Thompson1, K C Chou, C Zheng
1Department of Chemistry, Northern Illinois University, DeKalb 60115, USA.
Journal of Protein Chemistry
|October 1, 1995
Summary
Molecular dynamics simulations reveal that protein loops exhibit greater mobility and hydrophilic surface area than helices. This structural flexibility influences protein stability and interactions within folded protein structures.
Area of Science:
- Structural biology
- Computational biophysics
- Protein dynamics
Background:
- Alpha-helix bundle motifs are common protein structures.
- Understanding the mobility and stability of these motifs is crucial for protein function.
- Previous studies have focused on overall protein stability, but loop and helix-specific dynamics require further investigation.
Purpose of the Study:
- To investigate the structural mobility and stability of alpha-helix bundle motifs using molecular dynamics simulations.
- To analyze the contributions of loop-helix and helix-helix interactions to protein stability.
- To compare the solvent accessibility and electrostatic potentials of loop and helix regions.
Main Methods:
- Molecular dynamics simulations were performed on four representative proteins: methemerythrin, cytochrome b-562, cytochrome c', and bovine somatotropin.
- Energy analysis was used to compute loop-loop, helix-helix, and loop-helix interactions.
- The Eisenberg and McLachlan method was employed to calculate the percentage of hydrophilic solvent accessible area.
- Poisson-Boltzmann calculations were used to determine electrostatic potentials.
Main Results:
- Atomic RMS fluctuation was significantly larger in loop regions compared to helix regions across all studied proteins.
- In folded proteins, loop-helix interactions were stronger than helix-helix interactions, particularly due to electrostatic contributions.
- The stabilization energies from loop-helix and helix-helix interactions were comparable to each other but distinct from unfolded states.
- Protein-solvent interactions provided greater stabilization in helix regions than in loop regions.
- Loops exhibited a higher percentage of hydrophilic solvent accessible area than helices.
- Electrostatic potential calculations indicated that loops exert a more negative influence on helices than other helices do.
Conclusions:
- Protein loops are more mobile and possess greater hydrophilic character than alpha-helices.
- Loop-helix interactions play a significant role in the stability of folded alpha-helix bundle proteins.
- The interplay between internal interactions and protein-solvent interactions dictates overall protein stability.